Instructions ProMol Project Homology Models    v6
12/65/12
VDS

See: http://vdsstream.wikispaces.com/ProMol+Project

Purpose: make homology models for our enzymes that need them. We will use the ICM program on the DDFE because it seems to do a better job than just the SWISS-Model alone. 

On the Wikispaces page for this project, choose a protein which has not been taken. Type your name next to that protein and then continue on with the protocol.

Use SWISS-Model to predict template
	go to:  
	http://swissmodel.expasy.org/
	Choose Tools >> Template Identification:
	Input a Project Title:  e.g.  "Lmajor Template"
Copy and paste the Amino Acid sequence of the protein (can get from the Targets page on Wikispaces)
	Leave the defaults for the rest
	Wait. 
	Copy down the 4 or 5 digit PDB identifier for the Model.
	It will be 5 digit if it specifies a chaine of a multi chain model.  
	Type this ID into the Wikispaces page.
	Also Type the Identities % and Positives % into the Wikispaces.
	Download the actual PDB file for the template
	You will copy this over to the DDFE

Start up DDFE connection (WinSCP or SSH)
On DDFE make a folder of the name of the organism (e.g. Lmajor, Wbm, FtHap, YEPTP, Tbrucei, PfDXR, SAgalactiae, Lmonocytogenes): 
	/OrganismName      (e.g. /Lmajor)
	Make a folder within that called: 
	/OrganismName/ICMmodel		(e.g. /Lmajor/ICMmodel)
	

Use ICM to create homology itself
	Open Xming, XLaunch, then Putty
	Then go to the folder that you just made
	Type   $icm &    at the command prompt. 
	
	Use sequence of Target Protein for amino acid 
	Have to go to File >> New >> Sequence  and paste in the sequence.
		This will make a new object in the workspace panel on left

	Get the Template PDB (for whole protein or single chain)
		File >> Load PDB >> 
		enter the PDB 4 digit identifier identified in SWISS-Model
			e.g. 1SHS
		This will make a new object in the workspace panel on left
		If you need a single chain,
			then delete the chains you don't need on the left side 
			(could also do this in PyMol))
			OR go to NCBI Protein, Type in PDB_chain  

	Then Extract sequence of Template (right click on it in the left)
		This will make a new object in the workspace panel on left

	Select BOTH sequences in workspace, Right Click and ALign
		Or go to BIOINFO >> ALIGN TWO SEQUENCES

	Save your ICM project    File >> Save Project As >> ???.icb

	CREATE Homology Model with ICM
	Homology >> Build Model
		enter the seqeunce of your Target and the PDB of template
		Select the alignment that you just made in the steps above
		Do NOT Display results
		Minimize side chains
		Sample side chains
		Do NOT write object to file

	When it is done, a new ICM Object will be made. Right Click on it and Save As >> pdb (*.ent)
	** note This is tricky - Make Sure only the protein name is highlighted and not the Sequence beneath it. Otherwise you won't see the Save As pdb(*.ent) option.
	Name it something like:   ProteinNameICMHomology.ent

	Save your ICM project again    File >> Save Project As >> ???.icb


COMPARE QUALITY OF STRUCTURES USING MOLPROBITY
	ICMmodel vs. Template

Transfer your .ent model file to your local computer

Do Molprobity on .ent file from ICMmodel
-- don't add FLIPS, Do add H's,
-- Analyze All Atom Contacts and Geometry, Run programs,..
	Click on Multi-criterion CHART
	(Multi-criterion chart  - NOT the multi-criterion Kinemage!) 
	Save a copy of the Molprobity output chart as HTML file (be sure to only do the 'single-page' HTML file) 

Do Molprobity on template .pdb 
-- don't add FLIPS, Do add H's,
-- Analyze All Atom Contacts and Geometry, Run programs,..
	Click on Multi-criterion CHART
	(Multi-criterion chart  - NOT the multi-criterion Kinemage!) 
	Save a copy of the Molprobity output chart as HTML file (be sure to only do the 'single-page' HTML file) 





Transfer files to your DDFE for storage
Transfer file to Google Docs/ProMolProject for storage and review
	Make a new folder for your protein and put the files there
	Need these 3 files:
		ProteinNameICMHomology.ent
		Template's Molprobity output as single page HTML file 
		Homology Model's Molprobity output as single page HTML file 

On the Wikispaces page of ProMol Project
	Enter the Molprobity scores for both the Template and the Model:
	Template: Clash score, Molprobity score = ???, ???
	Model: Clash score, Molprobity score = ???, ???







